Autosomal dominant polycystic kidney disease (APKD), also called adult-onset polycystic kidney disease, is one of the most common hereditary disorders in humans, affecting approximately one individual in a thousand. The prevalence in the United States is greater than 500,000, with 6,000 to 7,000 new cases detected yearly (Striker et al., Am. J. Nephrol., 6:161-164, 1986; Iglesias et al., Am. J. Kid. Dis., 2:630-639, 1983). The disease is considered to be a systemic disorder, characterized by cyst formation in the ductal organs such as kidney, liver, and pancreas, as well as by gastrointestinal, cardiovascular, and musculoskeletal abnormalities, including colonic diverticulitis, berry aneurysms, hernias, and mitral valve prolapse (Gabow et al., Adv. Nephrol, 18:19-32, 1989; Gabow, New Eng. J. Med., 329:332-342, 1993).
The most prevalent and obvious symptom of APKD, however, is the formation of kidney cysts, which result in grossly enlarged kidneys and a decrease in renal-concentrating ability. Hypertension and endocrine abnormalities are also common in APKD patients, appearing even before symptoms of renal insufficiency. In approximately half of APKD patients, the disease progresses to end-stage renal disease; accordingly, APKD is responsible for 4-8% of the renal dialysis and transplantation cases in the United States and Europe (Proc. European Dialysis and Transplant Assn., Robinson and Hawkins, eds., 17: 20, 1981). Thus, there is a need in the art for diagnostic and therapeutic tools to reduce the incidence and severity of this discease.
APKD exhibits a transmission pattern typical of autosomal dominant inheritance, i.e. each offspring of an affected individual has a 50% chance of inheriting the causative gene. Linkage studies indicated that a causative gene is present on the short arm of chromosome 16, near the α-globin cluster; this locus was designated PKD1 (Reeders et al., Nature, 317:542, 1985.) Though other PKD-associated genes exist, such as, for example, PKD2, PKD1 defects appear to cause APKD in about 85-90% of affected families (Parfrey et al., New Eng. J. Med., 323:1085-1090, 1990; Peters et al., Contrib. Nephrol., 97:128-139, 1992).
The PKD1 gene has been localized to chromosomal position 16p13.3. Using extensive linkage analysis, in conjunction with the identification of new markers and restriction enzyme analysis, the gene has been further localized to an interval of approximately 600 kb between the markers ATPL and CMM65 (D16S84). The region is rich in CpG islands that are thought to flank transcribed sequences, and it has been estimated that this interval contains at least 20 genes. The precise location of the PKD1 gene was pinpointed by the finding of a PKD family whose affected members carry a translocation that disrupts a 14 kb RNA transcript associated with this region, as reported in the European PKD Consortium, Cell, 77:881, 1994. This article describes approximately 5 kb of DNA sequence corresponding to the 3′ end of the putative PKD1 cDNA sequence.
Notwithstanding knowledge of the partial PKD1 3′ cDNA sequence, several significant impediments stand in the way of determining the complete sequence of the PKD1 gene. For the most part, these impediments arise from the complex organization of the PKD1 locus. One serious obstacle is that sequences related to the PKD1 transcript are duplicated at least three times on chromosome 16 proximal to the PKD1 locus, forming PKD1 homologues. Another obstacle is that the PKD1 genomic interval also contains repeat elements that are present in other genomic regions. Both of these types of sequence duplications interfere with “chromosome walling” techniques that are widely used for identification of genomic DNA. This is because these techniques rely on hybridization to identify clones containing overlapping fragments of genomic DNA; thus, there is a high likelihood of “walking” into clones derived from PKD1 homologues instead of clones derived from the authentic PKD1 gene. In a similar manner, the PKD1 duplications and chromosome 16-specific repeats also interfere with the unambiguous determination of a complete cDNA sequence that encodes the PKD1 protein. Thus, there is a need in the art for genomic and cDNA sequences corresponding to the authentic PKD1 gene. This includes identification of segments of these sequences that are unique to the expressed PKD1 and not are present in the duplicated homologous sequences also present on chromosome 16.